mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 05:45:37 +08:00
Patch to upload.py for composite file uploads where the user supplies urls for components
At present, the path for each component is passed as a url and there's no upload type for composite file components, so this temporary fix searches for :// in the path to figure out if this is an url upload. Not ideal and in need of a more robust repair.
This commit is contained in:
+1
-1
@@ -7,7 +7,7 @@
|
||||
</head>
|
||||
<body>
|
||||
<div class="document">
|
||||
<div class="donemessagelarge">
|
||||
<div class="warningmessagelarge">
|
||||
<strong>Hello world! It's running...</strong>
|
||||
<hr>
|
||||
To customize this page edit <code>static/welcome.html</code>
|
||||
|
||||
@@ -298,12 +298,22 @@ def add_composite_file( dataset, json_file, output_path, files_path ):
|
||||
file_err( 'A required composite data file was not provided (%s)' % name, dataset, json_file )
|
||||
break
|
||||
elif dataset.composite_file_paths[value.name] is not None:
|
||||
dp = dataset.composite_file_paths[value.name][ 'path' ]
|
||||
isurl = dp.find('://') <> -1 # todo fixme
|
||||
if isurl:
|
||||
try:
|
||||
temp_name, dataset.is_multi_byte = sniff.stream_to_file( urllib.urlopen( dp ), prefix='url_paste' )
|
||||
except Exception, e:
|
||||
file_err( 'Unable to fetch %s\n%s' % ( dp, str( e ) ), dataset, json_file )
|
||||
return
|
||||
dataset.path = temp_name
|
||||
dp = temp_name
|
||||
if not value.is_binary:
|
||||
if dataset.composite_file_paths[ value.name ].get( 'space_to_tab', value.space_to_tab ):
|
||||
sniff.convert_newlines_sep2tabs( dataset.composite_file_paths[ value.name ][ 'path' ] )
|
||||
sniff.convert_newlines_sep2tabs( dp )
|
||||
else:
|
||||
sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] )
|
||||
shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( files_path, name ) )
|
||||
sniff.convert_newlines( dp )
|
||||
shutil.move( dp, os.path.join( files_path, name ) )
|
||||
# Move the dataset to its "real" path
|
||||
shutil.move( dataset.primary_file, output_path )
|
||||
# Write the job info
|
||||
|
||||
Reference in New Issue
Block a user